Autophagy modulates cell fate decisions during lineage commitment

Going through changes - the role of autophagy during reprogramming and differentiation

Somatic cell reprogramming is a complex feature that allows differentiated cells to undergo fate changes into different cell types. This process, which is conserved between plants and animals, is often achieved via dedifferentiation into pluripotent stem cells, which have the ability to generate all other types of cells and tissues of a given organism. Cellular reprogramming is thus a complex process that requires extensive modification at the epigenetic and transcriptional level, unlocking cellular programs that allow cells to acquire pluripotency. In addition to alterations in the gene expression profile, cellular reprogramming requires rearrangement of the proteome, organelles and metabolism, but these changes are comparatively less studied. In this context, autophagy, a cellular catabolic process that participates in the recycling of intracellular constituents, has the capacity to affect different aspects of cellular reprogramming, including the removal of protein signatures that might hamper reprogramming, mitophagy associated with metabolic reprogramming, and the supply of energy and metabolic building blocks to cells that undergo fate changes. In this Review, we discuss advances in our understanding of the role of autophagy during cellular reprogramming by drawing comparisons between plant and animal studies, as well as highlighting aspects of the topic that warrant further research.

Angiogenesis-on-a-chip coupled with single-cell RNA sequencing reveals spatially differential activations of autophagy along angiogenic sprouts

Several functions of autophagy associated with proliferation, differentiation, and migration of endothelial cells have been reported. Due to lack of models recapitulating angiogenic sprouting, functional heterogeneity of autophagy in endothelial cells along angiogenic sprouts remains elusive. Here, we apply an angiogenesis-on-a-chip to reconstruct 3D sprouts with clear endpoints. We perform single-cell RNA sequencing of sprouting endothelial cells from our chip to reveal high activation of autophagy in two endothelial cell populations- proliferating endothelial cells in sprout basements and stalk-like endothelial cells near sprout endpoints- and further the reciprocal expression pattern of autophagy-related genes between stalk- and tip-like endothelial cells near sprout endpoints, implying an association of autophagy with tip-stalk cell specification. Our results suggest a model describing spatially differential roles of autophagy: quality control of proliferating endothelial cells in sprout basements for sprout elongation and tip-stalk cell specification near sprout endpoints, which may change strategies for developing autophagy-based anti-angiogenic therapeutics.

Embryonic exposure of polystyrene nanoplastics affects cardiac development

Micro- and nanoplastics have recently been detected in human blood and placentas, indicating inevitable embryonic exposure to these particles. However, their influence on human embryogenesis and the underlying mechanisms are still unknown. In this study, the effects of polystyrene nanoplastics (PS-NPs) exposure on cardiac differentiation of human embryonic stem cells (hESCs) were evaluated. Uptake of PS-NPs not only caused cellular injury, but also regulated cardiac-related pathways as revealed by RNA-sequencing. Consequently, the efficiency of cardiomyocyte differentiation from hESCs was compromised, leading to immature of cardiomyocytes and smaller cardiac organoids with impaired contractility. Mechanistically, PS-NPs promoted mitochondrial oxidative stress, activated P38/Erk MAPK signaling pathway, blocked autophagy flux, and eventually reduced the pluripotency of hESCs. Consistently, in vivo exposure of PS-NPs from cleavage to gastrula period of zebrafish embryo led to reduced cardiac contraction and blood flow. Collectively, this study suggests that PS-NPs is a risk factor for fetal health, especially for heart development.

Effects of low doses of methylmercury (MeHg) exposure on definitive endoderm cell differentiation in human embryonic stem cells

Fetal development is one of the most sensitive windows to methylmercury (MeHg) toxicity. Laboratory and epidemiological studies have shown a dose-response relationship between fetal MeHg exposure and neuro performance in different life stages from infants to adults. In addition, MeHg exposure has been reported to be associated with disorders in endoderm-derived organs, such as morphological changes in liver cells and pancreatic cell dysfunctions. However, the mechanisms of the effects of MeHg on non-neuronal organs or systems, especially during the early development of endoderm-derived organs, remain unclear. Here we determined the effects of low concentrations of MeHg exposure during the differentiation of definitive endoderm (DE) cells from human embryonic stem cells (hESCs). hESCs were exposed to MeHg (0, 10, 100, and 200 nM) that covers the range of Hg concentrations typically found in human maternal blood during DE cell induction. Transcriptomic analysis showed that sub-lethal doses of MeHg exposure could alter global gene expression patterns during hESC to DE cell differentiation, leading to increased expression of endodermal genes/proteins and the over-promotion of endodermal fate, mainly through disrupting calcium homeostasis and generating ROS. Bioinformatic analysis results suggested that MeHg exerts its developmental toxicity mainly by disrupting ribosome biogenesis during early cell lineage differentiation. This disruption could lead to aberrant growth or dysfunctions of the developing endoderm-derived organs, and it may be the underlying mechanism for the observed congenital diseases later in life. Based on the results, we proposed an adverse outcome pathway for the effects of MeHg exposure during human embryonic stem cells to definitive endoderm differentiation.

Neural crest cells and fetal alcohol spectrum disorders: Mechanisms and potential targets for prevention

Fetal alcohol spectrum disorders (FASD) are a group of preventable and nongenetic birth defects caused by prenatal alcohol exposure that can result in a range of cognitive, behavioral, emotional, and functioning deficits, as well as craniofacial dysmorphology and other congenital defects. During embryonic development, neural crest cells (NCCs) play a critical role in giving rise to many cell types in the developing embryos, including those in the peripheral nervous system and craniofacial structures. Ethanol exposure during this critical period can have detrimental effects on NCC induction, migration, differentiation, and survival, leading to a broad range of structural and functional abnormalities observed in individuals with FASD. This review article provides an overview of the current knowledge on the detrimental effects of ethanol on NCC induction, migration, differentiation, and survival. The article also examines the molecular mechanisms involved in ethanol-induced NCC dysfunction, such as oxidative stress, altered gene expression, apoptosis, epigenetic modifications, and other signaling pathways. Furthermore, the review highlights potential therapeutic strategies for preventing or mitigating the detrimental effects of ethanol on NCCs and reducing the risk of FASD. Overall, this article offers a comprehensive overview of the current understanding of the impact of ethanol on NCCs and its role in FASD, shedding light on potential avenues for future research and intervention.

Autophagy-related gene and protein expressions during blastocyst development

PURPOSE

This study aims to examine the expression of autophagic genes and proteins during blastocyst development and differentiation.

METHODS

This is a prospective cohort study. Between March 2018 and November 2019, 30 females aged 30.13 ± 4.83 years underwent an intracytoplasmic sperm injection (ICSI) cycle at Madina Fertility Center. ICSI was used to develop and incubate 82 leftover embryos to day 5. Then, the embryos were divided into two groups based on their developmental structure: group D (n = 49) included embryos that developed into blastocysts, whereas group A (n = 33) included arrested embryos. These embryos were used to investigate the autophagic gene and protein expressions. The current study was approved by the Clinical Trial Ethical Committee of the Faculty of Medicine, Alexandria University, following the ethical standards of scientific research (Registration no. 0303721).

RESULTS

Embryos that developed into blastocysts on day 5 (group D) had significantly higher relative expression of the LC3 gene (1.11 ± 0.52) and beclin-1 gene (1.43 ± 0.34) and beclin-1 protein expression (3.8 ± 0.028) than those that did not develop into blastocysts on day 5 (group A) [0.72 ± 0.18 (P = 0.03), 0.35 ± 0.12 (P = 0.0001), and 3.14 ± 0.05, (P = 0.0001), respectively]. In contrast, mTOR and PIK3C3 protein expression was significantly higher in group A (arrested embryos) than those in group D (developed embryos) (P = 0.007 and P = 0.0001, respectively). Furthermore, the expression of the eIF4E gene was significantly lower in group D embryos (0.32 ± 0.07) than that in group A embryos (4.38 ± 1.16) (P = 0.0001).

CONCLUSIONS

This work identifies  autophagy as a well regulated process required to maintain cell allocation and differentiation during late preimplantation embryo developmental stages.

ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation

Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are critical for the naive-to-primed transition, and are also necessary for germline specification. RNA-seq and ATAC-seq profiling reveal that NANOG acts as a barrier to prevent pluripotency transition, and autophagy-dependent NANOG degradation is important for dismantling the naive pluripotency expression program through decommissioning of naive-associated active enhancers. Mechanistically, we found that autophagy receptor protein SQSTM1/p62 translocated into the nucleus during the pluripotency transition period and is preferentially associated with K63 ubiquitinated NANOG for selective protein degradation. In vivo, loss of autophagy by ATG7 depletion disrupts peri-implantation development and causes increased chromatin association of NANOG, which affects neuronal differentiation by competitively binding to OTX2-specific neuroectodermal development-associated regions. Taken together, our findings reveal that autophagy-dependent degradation of NANOG plays a critical role in regulating exit from the naive state and marks distinct cell fate allocation during lineage specification.Abbreviations: 3-MA: 3-methyladenine; EpiLC: epiblast-like cell; ESC: embryonic stem cell; PGC: primordial germ cell.